If we take this literally John Connor can't be Sarah's son. That doesn't mean he can't be the resistance leader he's supposed to become, of course, but it does suggest that something happened to Sarah's child (she's pregnant at the end of Terminator) and Sarah somehow adopted or stole another child to replace him.
So... let's assume that Sarah didn't stop in Mexico at the end of Terminator, she kept going and ended up in Britain. She miscarried somewhere along the way. And then, as if by a miracle, she found a child abandoned on the doorstep of a suburban home, and decided to raise him as John Connor...
Obvious fun stuff - "John" starts to learn combat techniques at an early age, and is already fairly kickass by the time of Terminator 2. Then in the aftermath of that owls start bombarding them with letters addressed to "Harry Potter" and Sarah has to admit the truth about her actions. Let's say this happens around the start of Terminator SCC, and Sarah sees this as a good way to get "John" out of the line of fire and get him some useful magical skills. Things are naturally complicated by the Terminators who are still hunting John and Sarah, by Cameron, Voldemort and Death Eaters etc. etc.
I'm not going to write this one, but maybe someone else would like to give it a try.